chromap = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/chromap"
bwa = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/bwa"
bowtie2 = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/bowtie2"
bowtie2index = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/bowtie2-build"
samtools = "/scratch/project/qaafi-cnafs/jingping/mamba/bin/samtools"
py2 = "/sw/local/rocky8.6/epyc3/qcif/software/miniconda3/envs/salsa2_2.3/bin/python2"
py3 = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/python3"
agp2assamble = "/scratch/project_mnt/S0030/jingping/software/juicebox_scripts/juicebox_scripts/agp2assembly.py"
matlock = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/matlock"
assamble2hic = "/scratch/project_mnt/S0030/jingping/software/3d-dna/visualize/run-assembly-visualizer.sh"
fastp = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/fastp"
samblaster = "/scratch/project_mnt/S0030/jingping/mamba/envs/haphic/bin/samblaster"
haphic_bin = "/scratch/project_mnt/S0030/jingping/software/HapHiC/"
minimap2 = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/minimap2"
hisat2 = "/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/hisat2"
chloGenome = ""
mitogenome = "/QRISdata/Q5822/Databases/mito_database/mitochondrion.1.1.genomic.fna"
BuildDatabase = ""
RepeatModeler = ""
RepeatMasker = ""